Contacts of the helix formed by residues 131 - 153 (chain B) in PDB entry 2P3Z
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 131 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A TYR 4.7 3.1 - - - -
126A TYR* 3.3 24.5 - - - -
128A GLY* 3.7 4.2 - - - -
130B GLY* 1.3 73.7 - - - -
132B LEU* 1.3 66.1 + - - -
134B MET* 2.9 6.1 + - - +
135B ASN* 2.9 32.9 + - - +
281B HIS 4.8 6.3 + - - -
305B TRP* 4.8 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A TYR* 2.7 27.1 + - + +
132A LEU* 3.9 27.8 - - + -
133A VAL* 4.2 13.7 - - + -
67B LEU* 4.1 11.9 - - + -
88B ALA* 3.8 35.0 - - + +
91B MET* 3.7 35.2 - - + -
92B GLY 4.6 1.8 - - - +
95B ILE* 4.6 6.3 - - + -
130B GLY 3.8 0.4 + - - -
131B GLY* 1.3 69.8 - - - -
133B VAL* 1.3 64.5 + - + +
135B ASN* 3.4 11.2 + - - +
136B THR* 3.0 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LEU* 4.2 13.5 - - + -
133A VAL* 6.2 0.7 - - + -
95B ILE* 3.9 21.1 - - + -
123B THR* 4.1 15.7 - - + +
126B TYR* 3.8 47.3 - - + +
127B SER* 3.7 29.8 + - - +
130B GLY 4.4 1.0 + - - -
131B GLY 3.1 1.0 + - - -
132B LEU* 1.3 78.4 - - + +
134B MET* 1.3 59.0 + - - +
136B THR* 3.2 4.3 + - - -
137B ILE* 3.0 29.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B LEU* 3.8 28.3 - - + -
127B SER* 4.1 21.3 + - - +
130B GLY* 3.6 24.9 + - - +
131B GLY 2.9 9.2 + - - +
133B VAL* 1.3 76.4 - - - +
135B ASN* 1.3 51.8 + - - +
137B ILE* 3.2 15.4 + - + +
138B SER* 2.8 40.7 + - - -
283B GLY* 4.3 3.6 - - - -
284B THR* 3.9 24.5 - - + -
305B TRP 3.4 20.0 - - - +
306B CYS 3.8 7.0 - - - +
307B GLY* 3.7 22.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A TYR 5.4 2.8 + - - -
126A TYR* 5.1 3.8 - - - +
67B LEU* 5.1 4.0 - - - +
86B SER* 3.7 5.8 + - - +
87B THR* 2.8 37.3 + - - +
88B ALA* 4.4 0.9 - - + -
131B GLY* 2.9 26.8 + - - +
132B LEU* 3.4 11.1 - - - +
134B MET* 1.3 74.5 - - - +
136B THR* 1.3 58.6 + - - +
138B SER 3.4 0.2 + - - -
139B CYS* 2.9 30.2 + - - +
304B GLY 3.2 13.3 - - - +
305B TRP* 3.2 43.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU* 4.0 11.6 - - + +
88B ALA* 3.7 4.9 - - - +
92B GLY* 3.5 26.7 - - - +
95B ILE* 3.7 26.4 - - + +
96B VAL* 3.5 29.2 - - + -
100B LEU* 4.4 2.7 - - + -
132B LEU* 3.0 12.9 + - - +
133B VAL* 3.4 9.2 - - - -
134B MET 3.1 0.8 - - - -
135B ASN* 1.3 75.6 - - - +
137B ILE* 1.3 64.8 + - - +
139B CYS* 3.2 3.6 + - - +
140B VAL* 3.0 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LEU* 4.2 10.3 - - + -
116B HIS* 4.2 19.3 - - + +
119B MET* 4.0 43.9 - - + +
120B LEU* 4.0 22.4 - - + -
123B THR* 3.4 26.7 - - + +
133B VAL* 3.0 23.9 + - + +
134B MET* 3.2 20.8 + - + +
136B THR* 1.3 78.3 - - - +
138B SER* 1.3 56.1 + - - +
140B VAL* 3.3 4.7 + - - +
141B ASP* 2.9 26.5 + - - +
307B GLY 4.4 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B MET 2.8 20.4 + - - -
135B ASN 3.4 0.2 - - - -
137B ILE* 1.3 69.2 - - - +
139B CYS* 1.3 66.4 + - - +
141B ASP* 3.2 2.6 + - - +
142B LEU* 2.9 30.4 + - - +
303B VAL 3.6 0.2 - - - -
304B GLY* 3.0 33.8 + - - -
305B TRP 3.5 2.8 - - - -
307B GLY 2.7 32.5 + - - -
308B GLY* 3.4 17.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU* 3.6 19.1 - - + -
72B VAL* 3.6 17.2 - - + +
84B ALA* 3.2 36.7 - - - +
85B VAL* 3.6 15.3 - - - -
86B SER* 3.7 11.4 - - - -
135B ASN 2.9 16.3 + - - +
136B THR 3.2 5.6 + - - +
138B SER* 1.3 78.1 - - - +
140B VAL* 1.3 61.1 + - - +
142B LEU* 3.5 6.7 + - - -
143B ALA* 3.0 22.9 + - - +
304B GLY 4.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B VAL* 4.2 18.4 - - + -
74B VAL* 5.2 2.7 - - + -
96B VAL* 4.0 23.8 - - + -
100B LEU* 4.3 13.7 - - + -
104B ILE* 3.7 29.4 - - + -
119B MET* 3.7 18.2 - - + -
136B THR 3.0 18.0 + - - +
137B ILE 3.6 6.5 - - - +
139B CYS* 1.3 74.5 - - - +
141B ASP* 1.3 59.2 + - - +
143B ALA* 3.2 3.3 + - - +
144B LEU* 2.9 40.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ILE* 3.6 12.3 - - - +
116B HIS* 3.6 23.8 - - + +
119B MET* 4.4 1.9 - - + +
137B ILE 2.9 14.2 + - - +
138B SER 3.6 7.4 - - - +
140B VAL* 1.3 74.7 - - - +
142B LEU* 1.3 61.9 + - - +
144B LEU* 3.2 12.9 + - - +
145B TRP* 3.0 32.3 + - - -
308B GLY* 4.0 6.7 - - - -
309B LEU 2.8 29.2 + - - -
310B THR* 2.6 32.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ALA* 3.4 20.4 - - + -
85B VAL 4.8 4.0 - - - +
138B SER 2.9 21.6 + - - +
139B CYS* 4.6 2.5 - - - -
141B ASP* 1.3 73.8 - - - +
143B ALA* 1.3 65.1 + - - +
145B TRP* 3.3 1.6 + - - +
146B ASP* 2.9 21.5 + - - +
303B VAL* 3.9 11.7 - - + +
304B GLY* 4.0 25.4 - - - +
308B GLY* 4.6 0.2 - - - -
309B LEU* 3.7 36.6 - - + +
334B TYR* 4.0 28.3 - - + -
389B PHE* 3.3 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B VAL* 3.7 27.6 - - + +
74B VAL* 3.9 21.1 - - + -
82B GLY 3.9 3.0 - - - +
83B PHE* 3.7 16.8 - - - -
84B ALA* 3.5 1.0 - - - +
139B CYS 3.0 14.8 + - - +
140B VAL 3.4 8.1 - - - +
142B LEU* 1.3 75.2 - - - +
144B LEU* 1.3 57.4 + - - +
146B ASP* 3.3 2.6 + - - +
147B LEU* 2.8 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ILE* 3.6 30.5 - - + -
74B VAL* 4.1 20.6 - - + -
104B ILE* 4.5 5.2 - - + -
109B VAL* 4.7 4.1 - - - +
112B ILE* 3.8 27.0 - - + +
115B ILE* 3.6 39.3 - - + -
119B MET* 4.7 1.8 - - + -
140B VAL* 2.9 29.7 + - + +
141B ASP* 3.5 11.2 - - - +
142B LEU 3.2 0.4 - - - -
143B ALA* 1.3 73.9 - - - +
145B TRP* 1.3 60.3 + - - +
147B LEU* 3.4 5.3 + - + +
148B PHE* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ILE* 3.4 31.4 - - + +
113B LYS* 5.4 11.0 - - + -
141B ASP* 3.0 35.2 + - - -
142B LEU 3.3 1.8 + - - +
144B LEU* 1.3 71.0 - - - +
146B ASP* 1.3 66.8 + - - +
148B PHE* 3.2 18.0 + + - +
149B GLY* 2.9 22.5 + - - -
156B VAL* 3.9 14.2 - - + +
159B LEU* 4.5 19.7 - - + -
160B LEU* 4.2 23.3 - - + -
309B LEU* 3.8 25.0 - - + +
310B THR* 2.9 33.6 + - + +
389B PHE* 3.7 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B GLY* 3.4 0.9 - - - -
83B PHE* 2.8 36.6 + - - +
142B LEU 2.9 14.2 + - - +
143B ALA 3.4 7.9 - - - +
145B TRP* 1.3 77.3 - - - +
147B LEU* 1.3 57.7 + - - +
149B GLY 3.3 0.2 + - - -
150B LYS* 2.7 68.0 + - - +
334B TYR* 6.0 0.2 - - - -
388B GLY* 3.5 4.5 - - - -
389B PHE* 2.8 44.1 + - + +
390B GLY 4.2 0.2 + - - -
391B VAL* 5.3 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ILE* 4.2 5.6 - - + -
74B VAL* 3.5 35.9 - - + +
76B ALA* 4.1 9.0 - - + +
80B GLN* 3.6 25.8 - - + +
81B THR 3.6 12.6 - - - +
82B GLY* 3.7 11.8 - - - +
109B VAL* 3.7 25.4 - - + -
143B ALA 2.8 19.7 + - - +
144B LEU* 3.8 5.6 - - + +
146B ASP* 1.3 72.3 - - - +
148B PHE* 1.3 58.1 + - - +
150B LYS* 3.2 3.6 + - + -
151B VAL* 2.8 43.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 3.9 22.9 - - + -
109B VAL* 3.7 27.6 - - + +
110B SER* 3.9 18.8 - - - -
112B ILE* 3.7 22.9 - - + -
144B LEU 2.9 18.7 + - - +
145B TRP* 3.6 11.2 - + - +
147B LEU* 1.3 77.6 - - - +
149B GLY* 1.3 52.2 + - - +
151B VAL* 3.2 3.9 + - + -
152B VAL* 2.9 59.6 + - + +
159B LEU* 3.8 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B TRP 2.9 12.9 + - - -
146B ASP 3.8 1.1 - - - -
148B PHE* 1.3 74.9 - - - +
150B LYS* 1.3 57.2 + - - +
152B VAL* 4.6 0.9 - - - -
153B GLY* 2.8 25.5 + - - -
154B LEU 2.9 31.0 + - - +
156B VAL* 5.1 0.9 - - - -
159B LEU* 3.9 15.6 - - - +
387B PRO* 3.8 0.7 - - - +
388B GLY* 3.4 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B GLN* 3.1 21.5 + - + +
81B THR 3.7 23.0 + - - +
82B GLY* 4.7 0.2 - - - -
83B PHE* 4.3 6.7 - - - -
146B ASP* 2.7 52.8 + - - +
147B LEU* 3.8 4.3 - - + +
148B PHE 3.1 0.2 - - - -
149B GLY* 1.3 76.0 - - - +
151B VAL* 1.3 63.3 + - - +
153B GLY* 3.5 8.3 + - - -
387B PRO* 3.7 35.4 - - + +
390B GLY* 4.7 2.0 - - - +
391B VAL 3.1 27.5 + - - +
392B GLU* 4.7 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B MET* 4.8 4.2 - - - +
6B THR 5.3 1.6 - - - +
7B LEU* 3.6 28.5 - - + -
8B PRO* 3.6 31.2 - - + -
78B ASN* 4.9 0.9 - - - +
80B GLN* 3.5 27.7 + - + +
109B VAL* 4.3 10.3 - - + -
147B LEU* 2.8 40.7 + - + +
148B PHE 3.7 4.3 - - - +
150B LYS* 1.3 74.4 - - - +
152B VAL* 1.3 63.3 + - - +
153B GLY* 4.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B MET* 4.0 32.2 - - + +
7B LEU* 4.1 13.7 - - + -
148B PHE* 2.9 49.8 + - + +
149B GLY 4.1 2.5 - - - +
151B VAL* 1.3 77.5 - - - +
153B GLY* 1.3 55.5 + - - +
154B LEU* 3.8 31.7 - - + +
159B LEU* 4.1 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B GLY 2.8 10.3 + - - -
150B LYS 3.5 6.0 + - - -
151B VAL 3.3 4.2 + - - -
152B VAL* 1.3 77.7 - - - +
154B LEU* 1.3 66.9 + - - +
155B PRO* 4.7 0.7 - - - +
387B PRO* 4.2 15.3 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il